Oligonucleotides have been used in various biological and biochemical applications. They have been used as primers and probes for the polymerase chain reaction (PCR), as antisense agents used in target validation, drug discovery and development, as ribozymes, as aptamers, and as general stimulators of the immune system. Antisense compounds have been used to modulate target nucleic acids. Antisense compounds comprising a variety of chemical modifications and motifs have been reported. In certain instances, such compounds are useful as research tools, diagnostic reagents, and as therapeutic agents. In certain instances antisense compounds have been shown to modulate protein expression by binding to a target messenger RNA (mRNA) encoding the protein. In certain instances, such binding of an antisense compound to its target mRNA results in cleavage of the mRNA. Antisense compounds that modulate processing of a pre-mRNA have also been reported. Such antisense compounds alter splicing, interfere with polyadenlyation or prevent formation of the 5′-cap of a pre-mRNA. Certain antisense compounds have undesired toxixity. See e.g., Swayze et al., “Antisense oligonucleotides containing locked nucleic acid improve potency but cause significant hepatotoxicity in animals” Nucleic Acid Research (2007) 35(2):687-700.). This widespread use of antisense compounds and their vast potential as a potent therapeutic platform has led to an increased demand for rapid, inexpensive, and efficient methods to analyze and quantify the in vitro and in vivo properties of these compounds.